Doctor Who: Curse of the Crystal Empire
by kukuruwataminesan
Summary: The Doctor's sad! He's been trying to cheer himself up after Amy and Rory's death, but he can't! Now, he's hoping that the ponies can cheer him up for a final time, before he gives up all hope! Set after The Angels Take Manhattan. Based on MLP: FiM: The Crystal Empire and told from the Doctor's point of view.
1. Chapter 1: An Urgent Message

Inside Canterlot Castle, Princess Celestia is checking documents with an assistant. Suddenly, a royal guard bursts in.

"News from Northern Equestria! Uh... Your Highness."

"Yes?" Princess Celestia replied.

"I am simply to tell you that _it_ has returned."

Princess Celestia turns to a royal guard. "Find Princess Cadance and Shining Armor." She turns to the other royal guard. "Get Princess Luna to summon the Doctor."

The royal guard asked, "Uh, which one?"

Princess Celestia said in an urgent tone, "All of them!" before the three guards run off. Meanwhile, Princess Celestia is writing a letter to Twilight Sparkle. "_My dearest Twilight, you must come to Canterlot at once._"


	2. Chapter 2: A Sad Time for the Doctor

The Doctor is in his TARDIS. His companions, Amy and Rory were long gone, taken back in time by the touch of a Weeping Angel, unable to save them in fear of a paradox.

During his time alone, the Doctor had done a lot of things. He went to the Wen Tao Gardens in Melbourne, Australia with Zhuge Liang and Mirai Suenaga, where he discovered more about the Time Lords secret from the Time War.

Next, he saved Tomoya Okazaki from the Dream Lord, almost risking his life and his TARDIS. In the end, he reunited him with his family, Nagisa and Ushio.

After, he discovered the Jenova Project with Zhuge Liang and his companion from his previous regeneration, Misao Kusakabe. They knew that Gallifreyan science was compatable with the project.

The Doctor also gained two companions, both from his previous regeneration. They were Tsukasa Hiiragi and Squid Girl (Squiddie). Tsukasa was his companion during the Parallax War and Squiddie had an adventure with him to the Kingdom of Salacia, where she met the kingdoms of sea creatures for the first time.

With Tsukasa and Squiddie, the Doctor helped Kouta Oyamada and Sōta Takanashi clean out the ghosts and monsters in Sōta's restuarant.

Next, they worked with Yuuta Togashi to help rediscover Rikka Takanashi's past.

Later, the Cardiff Rift opened, sending Yuki Yamaki, Shisei Nagato and their friends into Normal World (the Doctor's universe). The Doctor helped them get back into their own world while also solving a time anomaly between Saya Endo and Tsubomi Tachibana. Coincidentally, another anomaly occured between Yuki and Shisei.

The Doctor, Tsukasa and Squiddie had further adventures and the Doctor felt happier, but not really as much as the last time his companions left him.

Soon, the Doctor is about to take Tsukasa and Squiddie home when they are caught up in the Salacian Time War, first a mixture of parallel clones, each from a future that ended up differently. The Salacians planned to reveal themselves to the humans and use them as slaves, after Squid Girl failed her mission. It was because of what the humans were doing to the oceans; whaling and dumping rubbish into them that caused the Salacians to retaliate.

At the same time, Zhuge Liang is on another mission to save his brother from his girlfriend's cousin. He was dying and tried to regenerate, but couldn't. They discover some new family members: Zhuge Shu, part of the Mermaid Yakuza and a former Salacian, and Zhuge Qiao, a girl who helped save Amu Hinamori and her friends from the Dalek invasion of Earth. Yuki and Shisei also came back with their friends, two years after their last meeting from their point of view.

Zhuge Liang attempted to build a delta wave generator so that it would kill every single Salacian, but couldn't calibrate it to focus it only on the Salacians, therefore risking the fate of humanity and even time.

Meanwhile, Princess Celestia calls him to Cardiff, where with the help of Princess Luna, Twilight Sparkle and Amu Hinamori, create the Harmony Signal using the Elements of Harmony. It will send everyone back to their own worlds and seal off the Cardiff Rift. The signal is activated, but isn't getting through the rift.

Back at the TARDIS, with the help of Zhuge Liang's brother's girlfriend, Zhuge Liang's brother regenerates, with the new prototype sending the signal all over the universe. Zhuge Liang goes with the Doctor to help settle everyone back in and take Tsukasa and Squiddie home.

Later, Zhuge Liang and the Doctor tour the Jingzhou Innovation, Opportunity and Sustainability Centre at Teikyo University in Tochigi. They are attacked by armies from seven cities, but they successfully repel them.

The Mayans were right; the world would end on the 21st of December 2012, but luckily, the Doctor, with Zhuge Liang and his family, stopped the apocalypse and saved the Earth.

Yuki and Shisei came back again, two years from their point of view (again). The Doctor takes them back home after a confrontation in Cardiff.

Now, the Doctor is just alone, all by himself. He considers retiring because the universe doesn't want him anymore. But before he can do so, he sets the TARDIS for one final destination; Equestria.


	3. Chapter 3: Pony Time Lord Reunion

Doctor Whooves is in another TARDIS, with a Pegasus pony in an indigo coat and a rainbow for a cutie mark.

"What a day. We've stopped those sky pirates from throwing cats and dogs onto Earth!"

The Pony Doctor is in another TARDIS with the same design. He is with a Pegasus pony with a pinkish mane and a greenish coat.

"How did you know Storm Dasher was in love with you?"

"I don't know! The only pony who had a crush on me was somepony named Jee Gun or something. He had red eyes, a black mane and a pink tail. But suddenly, one day, he just disappeared!"

The Pony Doctor looked in confusion, trying to keep a secret. "Yeah, I don't know what happened to him either." He was the only normal pony/Time Lord who knew that Jee Gun regenerated into Storm Dasher.

* * *

Back in Doctor Whooves' TARDIS, he receives a signal. He traces it and the TARDIS materialises in the town square of Ponyville. The Pony Doctor and the Eleventh Doctor do too.

* * *

The Doctor is surprised to see Doctor Whooves and the Pony Doctor. They have a reunion hug and they catch up with their stories before they introduce him with their companions.

Doctor Whooves came up first. "Her name is Rainbowshine. She works in the weather factory in Cloudsdale."

"Pleased to meet you!" Rainbowshine said.

The Pony Doctor then showed his companion. "Doctor, this is Merry May. Jee Gun had a crush on her once, if you know what I mean." He winked and Merry May whacked him with her hoof.

Doctor Whooves wondered why the Doctor was alone. "Where are your companions? Where's Nayu?"

"She left me. She's safe now with her family and the Underwear Appreciation Society."

"And Kanade and Yuzuru?"

"Yuzuru's a medical officer at UNIT, and Kanade's just staying at home."

"What about Amy and Rory?"

Suddenly, the Doctor broke down in tears. Doctor Whooves said, "OK, so it wasn't a happy ending."

* * *

The three TARDISes received summon alerts. The Doctors went back into their TARDISes where they watched the message.

Princess Luna filmed and sent the message. It went: "Calling the Doctors. Calling any Doctors. Can you receive me? Can you receive me? If so, there is an emergency regarding a lost part of Equestria. If you receive the message, follow the coordinates to Canterlot. Your TARDIS will land in a parking lot, by which time you will be greeted by myself and be introduced to your mission. This is an emergency. I repeat, this is an emergency. Follow the coordinates to Canterlot and you will be greeted there. Transmission over."

The three TARDISes leave Ponyville, heading for Canterlot.


	4. Chapter 4: A Briefing and a Warning

*Doctor Who Series 6 Theme, with TARDIS materialisation sound at the end*

Matt Smith

Philip Zhou

*Doctor Who logo*

Curse of the Crystal Empire  
by Meghan McCarthy/kukuruwataminesan

* * *

The three TARDISes materialise in an area of Canterlot Castle. A group of royal guards greet them and escort them.

* * *

Meanwhile, Princess Celestia and Luna are talking.

"Are you sure you don't want me to go as well?"

Princess Celestia replied: "Yes. Princess Cadance and Shining Armor are already there. I'm sending out the Doctor to help them."

"The empire's magic is powerful. It cannot fall again, my sister."

"Trust me, little sister. The Doctor is a Time Lord, he should know how to deal with these sort of threats."

Twilight Sparkle comes in as Princess Luna leaves.

* * *

Princess Luna arrives at another building, where the three Doctors and their companions are waiting.

"Doctors, welcome to UNIT Equestria, formerly the Canterlot Security Department. We helped send Storm Dasher to you during the Medusa Cascade war, but how did Derpy get to you too?"

The Doctor didn't really want to say much. He just said, "Oh, it's complicated."

"Anyway, I have a favour to ask of you three. Do any one of you know anything about the Crystal Empire?" The Doctors said they didn't know about it.

Princess Luna uses a crystal to show the Doctors the Crystal Empire. "You wouldn't have known about anyway. Few remember it ever existed at all. Even my knowledge of the empire is limited. But what I do know is that it contains a powerful magic. One thousand years ago, King Sombra, a unicorn whose heart was black as night, took over the Crystal Empire." The Doctors are shown visions of the ponies subjected to slavery.

"He was ultimately overthrown, turned to shadow and banished to the ice of the arctic north. But not before he was able to put a curse upon the empire. A curse that caused it to vanish into thin air." The Empire disappears.

Princess Luna's eyes turn green, using black magic to show the Doctors. "If the empire is filled with hope and love, those things are reflected across all of Equestria. If hatred and fear take hold..." Black crystals surround the Doctors and their companions, but Princess Luna destroys them using her magic.

"Which is why I need your help finding a way to protect it." Princess Luna concluded.

The Pony Doctor is confused. "So, you want us to help protect an entire empire?"

Princess Luna continues, putting the crystal back to its original spot.. "There is one more danger, a danger that only Princess Celestia and I know. There were reports of spaceships falling near the Empire a thousand years ago. And inside, were... um... I've forgotten. I'm sorry, Doctors. Anyway, UNIT thinks that it's something left behind from the recent invasions. Your task is to go to the Empire and find out what is the source of the alien activity."

The Pony Doctor breathed a sigh of relief. "Whew! It's only a checking job. Consider it done, Princess!" The three Doctors go back to their TARDISes, but Princess Luna suddenly warns them of another thing.

"Remember, Doctors, from what I still remember, those aliens were really harsh on the ponies. There were a lot of ponies that died working in the Empire."

* * *

**Author's note: So, we've made it this far. That's alright.**


	5. Chapter 5: Evil of the Crystal Empire

Doctor Whooves, the Pony Doctor, Rainbowshine and Merry May travel to the Crystal Empire in the Doctor's TARDIS.

"So, what happened to Amy and Rory?" Doctor Whooves asked.

"Well, we were in New York for a picnic. We suddenly ended up in the 1930s. I saw River Song again. I could have saved them..." The Doctor started breaking into tears. "but, I couldn't change those points in time! They were fixed!" The Pony Doctor took over the controls as the others comforted him.

* * *

The TARDIS lands outside the Crystal Empire. The Pony Doctor checks the scanner.

"OK then, weather, windy and snowing, say minus 5 degrees. We've arrived, same day, same time, safe and sound."

Doctor Whooves looks on the large scanner. "I don't think we're safe and sound yet! I've got something weird on the scanner!"

* * *

Everypony and the Doctor go outside. The Doctor puts the TARDIS one second out of sync in case King Sombra were to steal it. Suddenly, dark energy is emerging from nearby.

The Doctor gets his sonic screwdriver out. "The Empire's that way! Everypony, run!"

Everyone runs as the life force of King Sombra is chasing them. The Doctor uses his screwdriver to distract it.

* * *

The ponies and the Doctor all walk inside a shield, leading to the Crystal Empire. Rainbowshine and Merry May marvel at the city in the distance.

Something is talking inside the Doctor's pocket. "Calling the Doctor, calling the Doctor..."

The Doctor takes out a disc inside his pocket, which is a hologram of Princess Luna. "If you've arrived safely, I want you to go inside the Crystal Palace to report to Princess Cadance and Shining Armor. If my timing is correct, Twilight Sparkle and her Ponyville friends should be arriving about now. Give this disc to them when you arrive and I'll explain to them about the situation while you continue with your task."


	6. Chapter 6: Cadance and the Time Lords

**Author's note: From now on, Doctor Whooves and the Pony Doctor (with their companions) will be mentioned as the 'ponies'.**

* * *

The ponies and the Doctor walk inside the Crystal Palace, just behind Twilight Sparkle and her friends, with another stallion about the same size as them, with an orange coat and purple mane...

"Storm Dasher!" The Pony Doctor called.

"Oh? Ah! Doctor, Doctor, Doctor, how very nice to see you all!"

Rainbow Dash told them, "I wanted him to stay in Ponyville, but he wanted to come with us!"

Doctor Whooves told her, "Well, he's part-Time Lord now! I think he can help you with complicated stuff like this!"

* * *

The Doctor and the ponies arrive in the main chamber, where Princess Cadance and Shining Armor greet them.

Twilight and Cadance greet each other with their song. "Sunshine, sunshine, ladybugs awake. Clap your hooves and do a little shake!"

Cadance replied, "One of these days we need to get together when the fate of Equestria _isn't_ hanging in the balance." She turned to the Doctor. "Oh, and Doctor? Thank you for helping me during my wedding day."

Twilight asks her if she is alright. Shining Armor explains, "Cadance has been able to use her magic to spread love and light. That seems to be what is protecting it. But she hasn't slept, barely eats. I want to help her, but my protection spell's been countered by King Sombra."

Even though Cadance says she is fine, Shining Armor continues. "She's _not_ fine. She can't go on like this forever, and if her magic were to fade, well, you saw what's out there waiting for that to happen."

Twilight says, "That's why we're here."

Storm Dasher adds, "Why we're all here!"

Shining Armor continues, "Well, with Cadance putting all her strength into keeping her spell going, and me trying to keep an eye on signs of trouble in the arctic, we haven't been able to gather much information from the Crystal Ponies. But we have to believe one of them knows how we can protect the empire without having to use Cadance's magic."

Twilight Sparkle suggests that they gather information from the Crystal Ponies and present it to them as a research paper.

As the others leave, Shining Armor calls Storm Dasher. "Uh, Dasher? Since you're part-Time Lord yourself, why don't you think up some ways to protect the empire?"

Dasher puts his brainy specs on and salutes. "Prince Shining Armor, I would be gladly honored to help you."

"You don't have to call me Prince Shining Armor."


	7. Chapter 7: King Sombra's Masters

The TARDIS lands just outside the cave. The Doctor puts the TARDIS one second out of sync again. The ponies and the Doctor go inside the cave.

The Pony Doctor hears a robotic sound. He puts on his stethoscope and goes to listen around the walls. He ends up at a door, and whatever he heard, shocked him greatly.

"The strategm is in place!"

"Prepare the spaceships! We will break the time-lock! The Daleks will return to the universe!"

All the Daleks started chanting, "The Daleks will return to the universe! The Daleks will return to the universe!"

The Pony Doctor suddenly backed away from the door, scared. "One thousand years of running, and this is what the Daleks have used the Empire for. I've been thick all this time! When I knew they weren't killing them..."

Doctor Whooves suddenly interrupted. "Um, Doctor, is there something you haven't told us about?"

* * *

The Doctor and the ponies sat down as the Pony Doctor gave his story.

"The story begins after my regeneration. I split into three and I was one of them. My TARDIS crash-landed in Canterlot and that was where I met Twilight Sparkle. After I solved a mystery in the library there, I travelled back in time to the foundation of Equestria. I saw Princesses Celestia and Luna take down Discord using the Elements of Harmony, with a little help from me, of course!"

"Then one day, I visited the Crystal Empire. I saw Dalek spaceships crash near a cave far away. I don't know if they were from the Parallax War, the Time War, or any war that I haven't seen at the time. I think the Pony Invasion and the Medusa Cascade War could have made this happen."

"Then suddenly, I saw King Sombra put the Crystal Ponies in slavery. I tried to talk him out of it, since at the time, he didn't even know what his ambition was for. Then, the day before he was going to let them go, the Daleks arrived."

"I ran to my TARDIS. I saw through the scanner the Daleks making King Sombra a pawn of them, to rebuild their spaceships and build new weapons. They saw my TARDIS and I quickly ran away as fast as I could. I wanted to be with Twilight Sparkle, but before that, I helped Princess Celestia defeat Luna and saw a zap apple harvest."

* * *

Meanwhile, back inside the Crystal Empire...

Twilight Sparkle is panicking. She can't find anything about the Crystal Heart. "I didn't know it was an actual relic! The book didn't mention anything about the crystal ponies powering the heart! There was a page missing... how did I not notice?!"

Tired, Princess Cadance suddenly faints. Her magic stops. The barrier starts to disappear. Black smoke begins to surround the city. King Sombra emerges...

* * *

Inside the Dalek cave...

"Alert! The barrier has been deactivated!"

"The strategem will commence! The Daleks will return to the universe! Exterminate the Crystal Empire!"

Then, every Dalek chanted, "Exterminate! Exterminate! Exterminate!"

* * *

**End of Part 1**


	8. Chapter 8: What's protecting the Empire?

Inside the Dalek cave, the door opens. The Daleks begin to emerge. The ponies and the Doctor run back to the TARDIS.

* * *

Meanwhile, back at the Crystal Empire...

Storm Dasher runs outside to report to Twilight Sparkle. "The Empire is under attack!"

Shining Armor helps Princess Cadance up. She reactivates the shield, cutting off King Sombra's horn in the process.

* * *

Back at the Dalek cave, the Daleks suddenly receive another alert.  
"Alert! The shield has been reactivated!"

"What is happening? Explain! Explain!"

* * *

By this time, the ponies and the Doctor have returned to the TARDIS, heading back to the Crystal Empire.

The Pony Doctor tells them, "The last time I was there, there was this thing in the middle of the castle, a Crystal Heart, the locals called it. Aha! That's what's been protecting the Empire! We've got to get the Heart back, right now before the Daleks do anything!"

* * *

Back at the Empire, Twilight tells Rainbow Dash to continue the Crystal Faire. Storm Dasher begins to fly off the top. "Dashie, wait for me!"

Rainbow Dash lands on the ground, with Storm Dasher landing after. "Why can't you stay in there and think of ways to protect the empire?"

"Because I heard what Twilight was telling Shining Armor about the Empire. The Crystal Heart's the only thing that's gonna help now. No Time Lord trick will work, it's not good enough. I'm going with Twilight to find the Heart. You just stay here, and do what you have to do." Storm Dasher flies off.

"Dasher! Dasher!"

* * *

Outside the Empire, a black crystal begins to grow...


	9. Chapter 9: Mission for the Crystal Heart

Dasher catches up with Twilight Sparkle. Spike is with her. "Twilight! I don't think you're going to be safe retrieving the Crystal Heart by yourself. I'm coming with you."

"You can't. I have to retrieve the Crystal Heart by myself."

"I know. I'm just going to protect you, like the Doctor used to. I'm not gonna put a hoof in!"

Twilight sighs. "Not a hoof, Dasher."

Twilight and Dasher begin running side by side. "So, where are we going exactly?"

"I think I might know where King Sombra hid the Crystal Heart."

"The castle?"

"The king would've been counting on the fact that nopony would dare come looking for it here. They'd've been too afraid to even try."

"I hope you're right."

"You and me both."

* * *

The TARDIS materialises inside the Crystal Palace. The Pony Doctor comes out. "Right, I think the Heart's going to be here. I just have to find it!"

Doctor Whooves interjects him. "WE just have to find it."

* * *

Meanwhile, Twilight, Spike and Dasher are running around, finding the Heart in every nook and cranny. "It's gotta to be here somewhere. It's just gotta be! Not a hoof, Dasher."

"I can't lift objects like you can. I'm only a Pegasus, but I'm not that stupid."

Suddenly, Twilight remembers what Princess Celestia told her. Then, the Doctor and the others find her. "Twilight!"

"Of course!"

Dasher suddenly stops. "What? Did you find it?"

"No, because _this _isn't King Sombra's castle?"

The Pony Doctor added, "But isn't this where he lived when he was in power?"

Twilight replied, "It is. But it didn't look like this." She uses the dark power, like Princess Luna showed the Doctor back at Canterlot. "That was a little trick Celestia taught me."

Suddenly, there is a flash, and Spike and Twilight disappear, leaving the ponies, Dasher and the Doctor. "Twilight? Twilight!"

Doctor Whooves noticed the Doctor didn't speak much. "Maybe we should go down here, Doctor?" They all went down the steps.

* * *

The Doctor takes his laser-sonic screwdriver out and turns it on, using it as a torch. They go down the steps.

* * *

Meanwhile, outside the Empire, King Sombra marvels at the crystals. The shield is failing.

* * *

The Daleks are using some sort of energy sucker in their base. "The shield is being sucked of its power!"

"Prepare the spaceships! We will use the Crystal Empire as a launch-pad! The Daleks will return to the universe!"

* * *

The Pony Doctor says, "We'll stay back up. You keep going down. You need anything, call for us!"

The Doctor musters up his courage and begins to run down the stairs. He trips, but he uses his laser-sonic screwdriver to turn himself upright.

The Doctor finds a door. It suddenly disappears. He uses the sonic function to open it, but it keeps running from him. He activates the laser function, and the door opens.

"Doctors? I think I've found the Heart!" He runs inside.


End file.
